Thinking...
We need to find details about pathway enrichment analysis from article. We must extract only what is explicitly reported. Let's analyze Methods:

In the Methods section:

"DEG analysis"

- They used DESeq to identify differential expression.
- GO enrichment analysis: performed by GOseq R package with corrected P-value ≤0.5 as cutoff. So tool: GOseq.

- KOBAS software used to test statistical enrichment of the DEGs in KEGG pathways.

"Comparison of expression patterns"

- STEM software used to identify temporal expression patterns of DEGs; GO and KEGG enrichment analysis also employed to identify potential functional genes or characterize expression profiles identified by STEM analysis.

Therefore, for pathway enrichment analysis, they used GOseq for GO enrichment, KOBAS for KEGG enrichment, perhaps STEM? But STEM used for temporal patterns not enrichment. In Results, they also mention "KOBAS software was used to test the statistical enrichment of the DEGs in the KEGG pathways."

So we need tool(s) used: GOseq, KOBAS. Versions? In Methods: GOseq R package with corrected P-value ≤0.5 as cutoff. No version given. KOBAS software used but no version. But we need to check if any version described.

Also earlier they used "KOBAS" maybe version? The Methods just say: "KOBAS software was used to test the statistical enrichment of the DEGs in the KEGG pathways." No version.

But also they might have used "GOseq" and "KOBAS" and "STEM". But STEM used for temporal expression patterns, not enrichment. But they may also used "GOseq" for GO enrichment; "KOBAS" for KEGG.

Now, "Which gene set libraries were used?" They used GO and KEGG. Maybe also "GOseq" uses GO. KOBAS uses KEGG. They may have used "CottonGen" for gene models but not for enrichment.

Thus gene set libraries: Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG).

"Does article describe using a custom or specific background gene list for enrichment analysis?" The article: "The DESeq R package (v1.18.0) was used to identify differential gene expression between the control and treatment" earlier. For background? Not described. Might mention: "DEGs were set as those genes with an adjusted P-value ≤0.01 as determined by DESeq." Not about background. So answer: Not described.

"Statistical test(s) used in enrichment analysis?" GOseq uses a correction for gene length; underlying test: hypergeometric test? In GOseq, the method uses a bias-corrected hypergeometric or GOseq's algorithm for gene set enrichment. But the article says: "GO enrichment analysis of the DEGs was performed by the GOseq R package with a corrected P-value ≤0.5 as the cutoff." That's just the tool. The test method is not described. So we must answer: Not described? Wait question: "What statistical test(s) were used in enrichment analysis?: State the name(s) of the statistical test(s) used for enrichment analysis (e.g., hypergeometric test, Fisher's exact test). Only include tests linked to enrichment."

The article does not mention any specific statistical test used by GOseq or KOBAS. They might rely on hypergeometric test but not specified. The Methods do not say. So answer: Not described.

"Was multiple testing correction / FDR applied to enrichment analysis?" The article mentions: "To manage the FDR, Benjamini and Hochberg’s approach was performed to adjust the obtained P-values." That was for DEG analysis, not for enrichment. For enrichment, they used "GOseq R package with a corrected P-value ≤0.5 as the cutoff." They didn't mention FDR for enrichment. But maybe they used "KOBAS software" with default p-value? But they didn't mention FDR. So answer: No.

But we should double-check if KOBAS uses FDR? It might have but article not mention. So answer No.

Now compile table:

Columns: Tool, Version, Gene Set Libraries, Custom background, Statistical test, Multiple testing correction.

Tool: GOseq, KOBAS.

Version: GOseq (not described). KOBAS (not described). So Not described.

Gene set libraries: GO, KEGG.

Custom background: Not described.

Statistical tests: Not described.

Multiple testing correction: No.

Let's produce table.

But the question: "What tool was used for pathway enrichment analysis?: List all tools or software packages used (e.g., DAVID, GSEA, Enrichr, etc.) that are explicitly mentioned in the article for enrichment analysis. Do not include tools used only for preprocessing (e.g., Salmon)." So GOseq and KOBAS.

"Was enrichment tool version(s) described?: List the version numbers associated with each enrichment tool, if reported." Not described.

"Which gene set libraries were used?": GO and KEGG.

"Does the article describe using a custom or specific background gene list for enrichment analysis?": Not described.

"What statistical test(s) were used in enrichment analysis?: State name(s) of statistical test(s) used for enrichment analysis (e.g., hypergeometric test, Fisher's exact test)." Not described.

"Was multiple testing correction / FDR applied to enrichment analysis?": No.

Let's ensure we don't misinterpret: They might have used "KOBAS" for KEGG. It is a tool for pathway enrichment. They didn't mention version. So "Not described".

Check: In Methods: "GO enrichment analysis of the DEGs was performed by the GOseq R package with a corrected P-value ≤0.5 as the cutoff. KOBAS software was used to test the statistical enrichment of the DEGs in the KEGG pathways." So tool names: GOseq, KOBAS.

Version: Not described.

Gene set libraries: GO, KEGG.

Custom background: Not described.

Statistical tests: Not described.

Multiple testing correction: No.

But hold on: In "DEG analysis" they used "Benjamini and Hochberg’s approach" to adjust the P-values. But that's for DEGs. Not for enrichment. So we should answer No for enrichment.

Ok produce table.

Let's produce 6 columns: Tool, Version(s), Gene set libraries, Custom background? (Yes/No/Not described), Statistical tests, Multiple testing correction.

We'll list each tool on separate rows: GOseq and KOBAS.

For GOseq, we can list gene set library as GO. For KOBAS, gene set library as KEGG.

But we might combine into one row per tool? The question: "List all tools or software packages used (e.g., DAVID, GSEA, Enrichr, etc.) that are explicitly mentioned in the article for enrichment analysis. If more than one tool, method, or database is used, list all of them separately." So each tool gets its own row. For each row, we need to fill columns accordingly. For GOseq row, version Not described, gene set library GO. Custom background: Not described. Statistical tests: Not described. Multiple testing correction: No. For KOBAS row: same.

Let's produce table.
...done thinking.

| Tool (enrichment analysis) | Version(s) described | Gene set libraries used | Custom/background list used? | Statistical test(s) used | Multiple testing correction applied? |
|------------------------------|----------------------|------------------------|---------------------------|--------------------------|-------------------------------------|
| GOseq (R package) | Not described | Gene Ontology (GO) | Not described | Not described | No |
| KOBAS | Not described | KEGG | Not described | Not described | No |